SNP pipeline analysis of subjects with 3 body site results
library(tidyverse)
source("MAP_functions.R")Subject 26
SNP_analysis_pipeline(subject_id = 26)[1] "SUBJECT_ID is 26"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 29845"
[1] "Num bases in R recomb = blocks 29845"
[1] "Num bases in V recomb = blocks 8898"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1036306"
[1] "Numbers of C bases above cutoff is 1036204"
[1] "Numbers of V bases above cutoff is 1035660"
[1] "Number of iSNP positions = 5311"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 36"
[1] "R only rare iSNPs (RonlyRIrare) = 16"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 4"
[1] "C only rare iSNPs (ConlyRIrare) = 0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 0"
[1] "V only rare iSNPs (VonlyRIrare) = 0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 6"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 0"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 2"
[1] "VC only rare iSNPs (VConlyRIrare) = 1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 5229"
[1] "All rare fixed SNPs (AllFrare) = 1179"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 22"
[1] "All iSNPs (AllRI) = 16"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 32
SNP_analysis_pipeline(subject_id = 32)[1] "SUBJECT_ID is 32"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 8083"
[1] "Num bases in R recomb = blocks 7903"
[1] "Num bases in V recomb = blocks 66553"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1035511"
[1] "Numbers of C bases above cutoff is 939599"
[1] "Numbers of V bases above cutoff is 1036507"
[1] "Number of iSNP positions = 5168"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 13"
[1] "R only rare iSNPs (RonlyRIrare) = 1"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 13"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 23"
[1] "C only rare iSNPs (ConlyRIrare) = 20"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 576"
[1] "V only rare iSNPs (VonlyRIrare) = 266"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 137"
[1] "RC only fixed SNPs (RConlyF) = 13"
[1] "RC only rare fixed SNPs (RConlyFrare) = 13"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 1"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 1"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 1"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 1"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 726"
[1] "All rare fixed SNPs (AllFrare) = 508"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 294"
[1] "All iSNPs (AllRI) = 11"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 1"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 68
SNP_analysis_pipeline(subject_id = 68)[1] "SUBJECT_ID is 68"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 66"
[1] "Num bases in R recomb = blocks 206"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1033503"
[1] "Numbers of C bases above cutoff is 1035903"
[1] "Numbers of V bases above cutoff is 1034542"
[1] "Number of iSNP positions = 5247"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 6"
[1] "R only rare iSNPs (RonlyRIrare) = 1"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 1"
[1] "C only rare iSNPs (ConlyRIrare) = 1"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 4"
[1] "V only rare iSNPs (VonlyRIrare) = 2"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 2"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 2"
[1] "VC only rare iSNPs (VConlyRIrare) = 1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 5189"
[1] "All rare fixed SNPs (AllFrare) = 1006"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 0"
[1] "All iSNPs (AllRI) = 11"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 72
SNP_analysis_pipeline(subject_id = 72)[1] "SUBJECT_ID is 72"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 73166"
[1] "Num bases in R recomb = blocks 73117"
[1] "Num bases in V recomb = blocks 65240"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 344563"
[1] "Numbers of C bases above cutoff is 1011352"
[1] "Numbers of V bases above cutoff is 1029389"
[1] "Number of iSNP positions = 617"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 49"
[1] "R only rare iSNPs (RonlyRIrare) = 44"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 0"
[1] "C only rare iSNPs (ConlyRIrare) = 0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 35"
[1] "V only rare iSNPs (VonlyRIrare) = 22"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 1"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 9"
[1] "RV only rare iSNPs (RVonlyRIrare) = 1"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 1"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 1"
[1] "VC only rare iSNPs (VConlyRIrare) = 1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 1"
[1] "All fixed SNPs (AllF) = 512"
[1] "All rare fixed SNPs (AllFrare) = 295"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 97"
[1] "All iSNPs (AllRI) = 1"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 87
SNP_analysis_pipeline(subject_id = 26)[1] "SUBJECT_ID is 26"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 29845"
[1] "Num bases in R recomb = blocks 29845"
[1] "Num bases in V recomb = blocks 8898"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1036306"
[1] "Numbers of C bases above cutoff is 1036204"
[1] "Numbers of V bases above cutoff is 1035660"
[1] "Number of iSNP positions = 5311"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 36"
[1] "R only rare iSNPs (RonlyRIrare) = 16"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 4"
[1] "C only rare iSNPs (ConlyRIrare) = 0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 0"
[1] "V only rare iSNPs (VonlyRIrare) = 0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 6"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 0"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 2"
[1] "VC only rare iSNPs (VConlyRIrare) = 1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 5229"
[1] "All rare fixed SNPs (AllFrare) = 1179"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 22"
[1] "All iSNPs (AllRI) = 16"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 98
SNP_analysis_pipeline(subject_id = 98)[1] "SUBJECT_ID is 98"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 245"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1038078"
[1] "Numbers of C bases above cutoff is 1004338"
[1] "Numbers of V bases above cutoff is 1035500"
[1] "Number of iSNP positions = 1301"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 27"
[1] "R only rare iSNPs (RonlyRIrare) = 15"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 2"
[1] "C only rare iSNPs (ConlyRIrare) = 2"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 47"
[1] "V only rare iSNPs (VonlyRIrare) = 39"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 31"
[1] "RV only rare iSNPs (RVonlyRIrare) = 3"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 0"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 1159"
[1] "All rare fixed SNPs (AllFrare) = 792"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 3"
[1] "All iSNPs (AllRI) = 3"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 107
SNP_analysis_pipeline(subject_id = 107)[1] "SUBJECT_ID is 107"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 0"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1036634"
[1] "Numbers of C bases above cutoff is 792534"
[1] "Numbers of V bases above cutoff is 1029789"
[1] "Number of iSNP positions = 3726"
[1] "R only fixed SNPs (RonlyF) = 2"
[1] "R only rare fixed SNPs (RonlyFrare) = 2"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 34"
[1] "R only rare iSNPs (RonlyRIrare) = 13"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 34"
[1] "C only rare iSNPs (ConlyRIrare) = 34"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 65"
[1] "V only rare iSNPs (VonlyRIrare) = 51"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 25"
[1] "RV only rare iSNPs (RVonlyRIrare) = 4"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 0"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 3546"
[1] "All rare fixed SNPs (AllFrare) = 674"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 0"
[1] "All iSNPs (AllRI) = 0"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 192
SNP_analysis_pipeline(subject_id = 192)[1] "SUBJECT_ID is 192"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 50904"
[1] "Num bases in R recomb = blocks 50443"
[1] "Num bases in V recomb = blocks 50443"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1036095"
[1] "Numbers of C bases above cutoff is 1028769"
[1] "Numbers of V bases above cutoff is 1037030"
[1] "Number of iSNP positions = 5297"
[1] "R only fixed SNPs (RonlyF) = 1"
[1] "R only rare fixed SNPs (RonlyFrare) = 1"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 20"
[1] "R only rare iSNPs (RonlyRIrare) = 13"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 2"
[1] "C only rare iSNPs (ConlyRIrare) = 2"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 1"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 64"
[1] "V only rare iSNPs (VonlyRIrare) = 51"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 3"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 2"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 46"
[1] "RV only rare iSNPs (RVonlyRIrare) = 7"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 1"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 1"
[1] "VC only rare iSNPs (VConlyRIrare) = 1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 5115"
[1] "All rare fixed SNPs (AllFrare) = 1215"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 63"
[1] "All iSNPs (AllRI) = 7"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 227
SNP_analysis_pipeline(subject_id = 227)[1] "SUBJECT_ID is 227"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 954"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 945"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 822591"
[1] "Numbers of C bases above cutoff is 1034715"
[1] "Numbers of V bases above cutoff is 1038235"
[1] "Number of iSNP positions = 999"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 178"
[1] "R only rare iSNPs (RonlyRIrare) = 149"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 0"
[1] "C only rare iSNPs (ConlyRIrare) = 0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 0"
[1] "V only rare iSNPs (VonlyRIrare) = 0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 0"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 3"
[1] "VC only rare iSNPs (VConlyRIrare) = 1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 798"
[1] "All rare fixed SNPs (AllFrare) = 540"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 15"
[1] "All iSNPs (AllRI) = 4"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 362
SNP_analysis_pipeline(subject_id = 362)[1] "SUBJECT_ID is 362"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 0"
[1] "Num bases in R recomb = blocks 160315"
[1] "Num bases in V recomb = blocks 160315"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1031572"
[1] "Numbers of C bases above cutoff is 1032552"
[1] "Numbers of V bases above cutoff is 1038383"
[1] "Number of iSNP positions = 2002"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 10"
[1] "R only rare iSNPs (RonlyRIrare) = 9"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 1"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 4"
[1] "C only rare iSNPs (ConlyRIrare) = 4"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 3"
[1] "V only rare iSNPs (VonlyRIrare) = 2"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 5"
[1] "RV only rare iSNPs (RVonlyRIrare) = 1"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 1"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 1"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 1944"
[1] "All rare fixed SNPs (AllFrare) = 879"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 790"
[1] "All iSNPs (AllRI) = 13"
[1] "All rare iSNPs (AllRIrare) = 1"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 2"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 519
SNP_analysis_pipeline(subject_id = 519)[1] "SUBJECT_ID is 519"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 431"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 226"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 818552"
[1] "Numbers of C bases above cutoff is 1020321"
[1] "Numbers of V bases above cutoff is 1034717"
[1] "Number of iSNP positions = 3957"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 27"
[1] "R only rare iSNPs (RonlyRIrare) = 27"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 1"
[1] "C only rare iSNPs (ConlyRIrare) = 0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 3"
[1] "V only rare iSNPs (VonlyRIrare) = 2"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 0"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 0"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 3913"
[1] "All rare fixed SNPs (AllFrare) = 780"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 17"
[1] "All iSNPs (AllRI) = 4"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 564
SNP_analysis_pipeline(subject_id = 564)[1] "SUBJECT_ID is 564"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 0"
[1] "Num bases in R recomb = blocks 24734"
[1] "Num bases in V recomb = blocks 24734"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1035161"
[1] "Numbers of C bases above cutoff is 1030082"
[1] "Numbers of V bases above cutoff is 1013781"
[1] "Number of iSNP positions = 5253"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 0"
[1] "R only rare iSNPs (RonlyRIrare) = 0"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 231"
[1] "C only rare fixed SNPs (ConlyFrare) = 57"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 126"
[1] "C only iSNPs (ConlyRI) = 4"
[1] "C only rare iSNPs (ConlyRIrare) = 4"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 58"
[1] "V only rare iSNPs (VonlyRIrare) = 53"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 1"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 179"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 96"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 78"
[1] "RV only iSNPs (RVonlyRI) = 1"
[1] "RV only rare iSNPs (RVonlyRIrare) = 1"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 0"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 4668"
[1] "All rare fixed SNPs (AllFrare) = 881"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 32"
[1] "All iSNPs (AllRI) = 7"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 753
SNP_analysis_pipeline(subject_id = 753)[1] "SUBJECT_ID is 753"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 0"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 619998"
[1] "Numbers of C bases above cutoff is 1037605"
[1] "Numbers of V bases above cutoff is 1037470"
[1] "Number of iSNP positions = 912"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 233"
[1] "R only rare iSNPs (RonlyRIrare) = 105"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 1"
[1] "C only rare iSNPs (ConlyRIrare) = 1"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 0"
[1] "V only rare iSNPs (VonlyRIrare) = 0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 1"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 0"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 2"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 623"
[1] "All rare fixed SNPs (AllFrare) = 426"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 0"
[1] "All iSNPs (AllRI) = 6"
[1] "All rare iSNPs (AllRIrare) = 2"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 908
SNP_analysis_pipeline(subject_id = 908)[1] "SUBJECT_ID is 908"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 0"
[1] "Num bases in R recomb = blocks 700"
[1] "Num bases in V recomb = blocks 494"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1033470"
[1] "Numbers of C bases above cutoff is 1032274"
[1] "Numbers of V bases above cutoff is 1006412"
[1] "Number of iSNP positions = 5112"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 0"
[1] "R only rare iSNPs (RonlyRIrare) = 0"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 15"
[1] "C only rare iSNPs (ConlyRIrare) = 6"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 86"
[1] "V only rare iSNPs (VonlyRIrare) = 80"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 2"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 1"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 0"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 4852"
[1] "All rare fixed SNPs (AllFrare) = 928"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 8"
[1] "All iSNPs (AllRI) = 6"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 927
SNP_analysis_pipeline(subject_id = 927)[1] "SUBJECT_ID is 927"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 37976"
[1] "Num bases in R recomb = blocks 37162"
[1] "Num bases in V recomb = blocks 37632"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1026496"
[1] "Numbers of C bases above cutoff is 1034845"
[1] "Numbers of V bases above cutoff is 1034464"
[1] "Number of iSNP positions = 5283"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 2"
[1] "R only rare iSNPs (RonlyRIrare) = 0"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 0"
[1] "C only rare iSNPs (ConlyRIrare) = 0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 4"
[1] "V only rare iSNPs (VonlyRIrare) = 0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 1"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 1"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 1"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 1"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 0"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 5244"
[1] "All rare fixed SNPs (AllFrare) = 1247"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 183"
[1] "All iSNPs (AllRI) = 24"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 5"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 951
SNP_analysis_pipeline(subject_id = 951)[1] "SUBJECT_ID is 951"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 14329"
[1] "Num bases in R recomb = blocks 16927"
[1] "Num bases in V recomb = blocks 14329"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1013234"
[1] "Numbers of C bases above cutoff is 1035195"
[1] "Numbers of V bases above cutoff is 1035300"
[1] "Number of iSNP positions = 5191"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 14"
[1] "R only rare iSNPs (RonlyRIrare) = 2"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 2"
[1] "C only rare iSNPs (ConlyRIrare) = 1"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 8"
[1] "V only rare iSNPs (VonlyRIrare) = 1"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 1"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 0"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 2"
[1] "VC only rare iSNPs (VConlyRIrare) = 2"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 5069"
[1] "All rare fixed SNPs (AllFrare) = 1083"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 106"
[1] "All iSNPs (AllRI) = 17"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 1077
SNP_analysis_pipeline(subject_id = 1077)[1] "SUBJECT_ID is 1077"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 10689"
[1] "Num bases in R recomb = blocks 9806"
[1] "Num bases in V recomb = blocks 10291"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 798730"
[1] "Numbers of C bases above cutoff is 1036188"
[1] "Numbers of V bases above cutoff is 979111"
[1] "Number of iSNP positions = 3956"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 154"
[1] "R only rare iSNPs (RonlyRIrare) = 109"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 14"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 0"
[1] "C only rare iSNPs (ConlyRIrare) = 0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 59"
[1] "V only rare iSNPs (VonlyRIrare) = 47"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 1"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 2"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 1"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 1"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 0"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 3145"
[1] "All rare fixed SNPs (AllFrare) = 620"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 104"
[1] "All iSNPs (AllRI) = 6"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 2"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 1078
SNP_analysis_pipeline(subject_id = 1078)[1] "SUBJECT_ID is 1078"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 0"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 26229"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 875018"
[1] "Numbers of C bases above cutoff is 249618"
[1] "Numbers of V bases above cutoff is 1015869"
[1] "Number of iSNP positions = 1382"
[1] "R only fixed SNPs (RonlyF) = 96"
[1] "R only rare fixed SNPs (RonlyFrare) = 40"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 4"
[1] "R only iSNPs (RonlyRI) = 103"
[1] "R only rare iSNPs (RonlyRIrare) = 65"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 12"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 85"
[1] "C only rare iSNPs (ConlyRIrare) = 74"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 4"
[1] "V only fixed SNPs (VonlyF) = 1"
[1] "V only rare fixed SNPs (VonlyFrare) = 1"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 35"
[1] "V only rare iSNPs (VonlyRIrare) = 34"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 1"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 33"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 91"
[1] "RV only rare iSNPs (RVonlyRIrare) = 5"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 9"
[1] "VC only fixed SNPs (VConlyF) = 4"
[1] "VC only rare fixed SNPs (VConlyFrare) = 2"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 17"
[1] "VC only rare iSNPs (VConlyRIrare) = 10"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 1"
[1] "All fixed SNPs (AllF) = 32"
[1] "All rare fixed SNPs (AllFrare) = 32"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 0"
[1] "All iSNPs (AllRI) = 65"
[1] "All rare iSNPs (AllRIrare) = 1"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 2"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 1079
SNP_analysis_pipeline(subject_id = 1079)[1] "SUBJECT_ID is 1079"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 24626"
[1] "Num bases in R recomb = blocks 25420"
[1] "Num bases in V recomb = blocks 24894"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1018215"
[1] "Numbers of C bases above cutoff is 1036824"
[1] "Numbers of V bases above cutoff is 1035527"
[1] "Number of iSNP positions = 5450"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 299"
[1] "R only rare iSNPs (RonlyRIrare) = 137"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 3"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 2"
[1] "C only rare iSNPs (ConlyRIrare) = 0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 22"
[1] "V only rare iSNPs (VonlyRIrare) = 8"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 2"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 2"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 19"
[1] "RV only rare iSNPs (RVonlyRIrare) = 1"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 1"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 2169"
[1] "All rare fixed SNPs (AllFrare) = 858"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 104"
[1] "All iSNPs (AllRI) = 7"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 1106
SNP_analysis_pipeline(subject_id = 1106)[1] "SUBJECT_ID is 1106"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 21790"
[1] "Num bases in R recomb = blocks 21569"
[1] "Num bases in V recomb = blocks 3423"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1024517"
[1] "Numbers of C bases above cutoff is 1032626"
[1] "Numbers of V bases above cutoff is 1038242"
[1] "Number of iSNP positions = 692"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 0"
[1] "R only rare iSNPs (RonlyRIrare) = 0"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 0"
[1] "C only rare iSNPs (ConlyRIrare) = 0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 1"
[1] "V only rare iSNPs (VonlyRIrare) = 1"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 1"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 1"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 1"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 0"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 0"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 667"
[1] "All rare fixed SNPs (AllFrare) = 425"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 138"
[1] "All iSNPs (AllRI) = 6"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 1"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 1145
SNP_analysis_pipeline(subject_id = 1145)[1] "SUBJECT_ID is 1145"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 474"
[1] "Num bases in R recomb = blocks 261"
[1] "Num bases in V recomb = blocks 177"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1026277"
[1] "Numbers of C bases above cutoff is 1034922"
[1] "Numbers of V bases above cutoff is 888302"
[1] "Number of iSNP positions = 4468"
[1] "R only fixed SNPs (RonlyF) = 1"
[1] "R only rare fixed SNPs (RonlyFrare) = 1"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 3"
[1] "R only rare iSNPs (RonlyRIrare) = 2"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 1"
[1] "C only rare iSNPs (ConlyRIrare) = 1"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 139"
[1] "V only rare iSNPs (VonlyRIrare) = 116"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 2"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 1"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 0"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 4155"
[1] "All rare fixed SNPs (AllFrare) = 780"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 19"
[1] "All iSNPs (AllRI) = 7"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 1176
SNP_analysis_pipeline(subject_id = 1176)[1] "SUBJECT_ID is 1176"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 46106"
[1] "Num bases in R recomb = blocks 21526"
[1] "Num bases in V recomb = blocks 4302"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1038149"
[1] "Numbers of C bases above cutoff is 1035843"
[1] "Numbers of V bases above cutoff is 1027021"
[1] "Number of iSNP positions = 6142"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 62"
[1] "R only rare iSNPs (RonlyRIrare) = 29"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 40"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 6"
[1] "C only rare iSNPs (ConlyRIrare) = 2"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 1"
[1] "V only fixed SNPs (VonlyF) = 1"
[1] "V only rare fixed SNPs (VonlyFrare) = 1"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 528"
[1] "V only rare iSNPs (VonlyRIrare) = 303"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 45"
[1] "RC only fixed SNPs (RConlyF) = 53"
[1] "RC only rare fixed SNPs (RConlyFrare) = 25"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 330"
[1] "RC only rare iSNPs (RConlyRIrare) = 90"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 165"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 18"
[1] "RV only rare iSNPs (RVonlyRIrare) = 5"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 7"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 0"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 380"
[1] "All rare fixed SNPs (AllFrare) = 372"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 36"
[1] "All iSNPs (AllRI) = 322"
[1] "All rare iSNPs (AllRIrare) = 88"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 82"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 1182
SNP_analysis_pipeline(subject_id = 1182)[1] "SUBJECT_ID is 1182"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 0"
[1] "Num bases in R recomb = blocks 9959"
[1] "Num bases in V recomb = blocks 22563"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1036038"
[1] "Numbers of C bases above cutoff is 1029053"
[1] "Numbers of V bases above cutoff is 1035249"
[1] "Number of iSNP positions = 5725"
[1] "R only fixed SNPs (RonlyF) = 20"
[1] "R only rare fixed SNPs (RonlyFrare) = 13"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 361"
[1] "R only rare iSNPs (RonlyRIrare) = 165"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 36"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 10"
[1] "C only rare iSNPs (ConlyRIrare) = 7"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 5"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 2"
[1] "V only rare iSNPs (VonlyRIrare) = 2"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 19"
[1] "RV only rare iSNPs (RVonlyRIrare) = 8"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 3"
[1] "VC only fixed SNPs (VConlyF) = 470"
[1] "VC only rare fixed SNPs (VConlyFrare) = 207"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 46"
[1] "VC only iSNPs (VConlyRI) = 27"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 10"
[1] "All fixed SNPs (AllF) = 241"
[1] "All rare fixed SNPs (AllFrare) = 218"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 60"
[1] "All iSNPs (AllRI) = 3"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 1201
SNP_analysis_pipeline(subject_id = 1201)[1] "SUBJECT_ID is 1201"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 173"
[1] "Num bases in R recomb = blocks 256"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1038120"
[1] "Numbers of C bases above cutoff is 1025145"
[1] "Numbers of V bases above cutoff is 1037114"
[1] "Number of iSNP positions = 1147"
[1] "R only fixed SNPs (RonlyF) = 1"
[1] "R only rare fixed SNPs (RonlyFrare) = 1"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 11"
[1] "R only rare iSNPs (RonlyRIrare) = 2"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 0"
[1] "C only rare iSNPs (ConlyRIrare) = 0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 0"
[1] "V only rare iSNPs (VonlyRIrare) = 0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 0"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 2"
[1] "VC only rare iSNPs (VConlyRIrare) = 1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 1086"
[1] "All rare fixed SNPs (AllFrare) = 729"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 11"
[1] "All iSNPs (AllRI) = 10"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
Subject 1226
SNP_analysis_pipeline(subject_id = 1226)[1] "SUBJECT_ID is 1226"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 3764"
[1] "Num bases in R recomb = blocks 3764"
[1] "Num bases in V recomb = blocks 3764"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1018587"
[1] "Numbers of C bases above cutoff is 1035547"
[1] "Numbers of V bases above cutoff is 1033213"
[1] "Number of iSNP positions = 5206"
[1] "R only fixed SNPs (RonlyF) = 1"
[1] "R only rare fixed SNPs (RonlyFrare) = 1"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 26"
[1] "R only rare iSNPs (RonlyRIrare) = 22"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 2"
[1] "C only rare iSNPs (ConlyRIrare) = 2"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 2"
[1] "V only rare iSNPs (VonlyRIrare) = 2"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 0"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 1"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 5134"
[1] "All rare fixed SNPs (AllFrare) = 1056"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 31"
[1] "All iSNPs (AllRI) = 24"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
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